Arabimarklet: Tools to Jump across Arabidopsis Databases
When you are at ANY website that contains At0g00000-type gene codes, .
How to Use
1. Right-click a link to your favorite website and select "Add to Favorites" (Internet Explorer) or "Bookmark this link" (Firefox) to bookmark it. If you use Safari or Chrome, please drag-and-drop the link to the bookmark bar.
2. Visit ANY website that contains Arabidopsis gene IDs.
- eg http://atted.jp/data/locus/At2g37130.shtml (in URL) or http://www.ncbi.nlm.nih.gov/protein/15221314 (in page content)
3. Open that bookmark! (You may need to allow pop-up windows.)
If you wish to test how these Arabimarklets work...
Just please left-click the links.
They will automatically find gene ID(s) in the page content (see 4 lines above!) and immediately bring you to the corresponding entry in the selected database.
Arabimarklets do the same wherever you are.
Comprehensive Arabidopsis information resource.
Sequence-centered genome view, with a narrow focus on gene structure annotation.
Microarray data and sample descriptions from the AtGenExpress project.
Genome-wide map of potential transcription factor and small RNA binding sites.
Proteome database with a proteogenomic mapping of the peptides onto the genome.
Gene coexpression database (Arabidopsis Thaliana Trans-factor and cis-Element prediction Database).
Website for exploring microarray and other data for hypothesis generation (Electronic fluorescent pictographic browser). Part of Bio-Array Resource for Plant Functional Genomics (BAR).
Databases of homologous proteins, automatically constructed but from a biologist's viewpoint.
A user-friendly expression visualization tool, bringing gene expression into the context of thousands of conditions.
Gene Ontology database.
Eukaryotic ortholog group database.
Kazusa Arabidopsis thaliana Annotation Abstract, containing information and annotations of genes and proteins, gene families, gene ontology terms, metabolic pathways and gene expression data.
Kyoto Encyclopedia of Genes and Genomes.
Comprehensive Arabidopsis thaliana Database at MIPS (Munich Information Center for Protein Sequences).
MPSS (Massively parallel signature sequencing) mRNA tags (DpnII) and MPSS/454 small RNA data at University of Delaware.
To NASCArrays Digital Northern
To NASCArrays Spot History
Tools showing how genes are expressed over all the experiments in the Nottingham Arabidopsis Stock Centre's microarray database.
To NCBI Gene
Gene database at NCBI.
To NCBI AceView
A curated, comprehensive and non-redundant sequence representation of all public mRNA sequences.
Plant Genome Duplication Database, to identify and catalog plant genes in terms of intragenome or cross-genome syntenic relationships.
Database of clusters of orthologous and paraloous genes.
A comprehensive plant biochemical pathway database.
Comparative genomics resource to study gene and genome evolution in plants.
Plant Proteome DataBase, storing experimental data from in-house proteome and mass spectrometry analysis, curated information about protein function, protein properties and subcellular localization.
To RTSF Microarray Viewer
Arabidopsis developmental microarray data from the AtGenExpress Consortium, at Research Technology Support Facility, Michigan State University.
Proteome database, containing protein motif structure and phylogenetic information.
To Salk SNP Viewer
Arabidopsis SNP Sequence Viewer at Salk Institute.
SBS (Sequencing By Synthesis) mRNA tags (DpnII) and MPSS/454 small RNA data at University of Delaware.
A visual data mining front end for exploring correlation networks constructed from microarray data.
SubCellular Proteomic Database, housing large scale proteomic and GFP localisation sets from cellular compartments of Arabidopsis.
To T-DNA Express
Arabidopsis Gene Mapping Tool at Salk Institute.
Tiling array data with ATH1 array data.
Please email firstname.lastname@example.org (Wataru IWASAKI) or tweet to me in English or Japanese if you need bookmarklets to other databases or found any problems regarding these tools.
They do not do anything other than opening new browser windows, and have no security risks.
Arabimarklets do not work on Internet Explorer 6.
[Sep 28 2010] Address corrected: To AtGDB
[Sep 23 2010] Database added: To StarNet2
[Sep 16 2010] Version 3.1 released: Performance improved.
[Sep 12 2010] Version 3.0 released: now Arabimarklets can handle cases that more than 6 gene IDs are found.
[Sep 9 2010] Databases added: To Genevestigator, To NCBI Gene, To NCBI AceView, To PGDD, To PlantCyc, and To PPDB
[Sep 9 2010] Version 2.2 released: now Arabimarklets convert gene IDs to the At*g***** case style.
[Sep 8 2010] Version 2.1 released: now Arabimarklets open up to 5 windows even if more IDs are found.
[Sep 7 2010] Version 2.0 released: now Arabimarklets (1) search page content if URLs do not contain Gene IDs and (2) open multiple windows if multiple IDs are found.
[Sep 7 2010] Database added: To Gclust
[Sep 6 2010] Databases added: To GO and To KEGG
[Sep 4 2010] Version 1.0 released.